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関連する概念動画

RNA Structure01:23

RNA Structure

78.7K
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
78.7K
RNA Structure01:19

RNA Structure

7.1K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
7.1K
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

44.9K
VSEPR Theory for Determination of Electron Pair Geometries
44.9K
Nucleic Acid Structure01:25

Nucleic Acid Structure

8.4K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
8.4K
RNA Stability01:53

RNA Stability

35.6K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
35.6K
Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.0K

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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RNA構造における原子レベルの柔軟性を予測するための深層学習ベースの自動化アプローチ：DeepRMSF

Chenjie Feng1, Xiaowen Sun2, Xintao Song2

  • 1College of Medical Information and Engineering, Ningxia Medical University, No. 1160 Shengli Road, Xingqing District, Yinchuan, Ningxia Province 750004, China.

Briefings in bioinformatics
|January 13, 2026
PubMed
まとめ

新しい深層学習手法であるDeepRMSFは、構造からRNAの振動柔軟性を正確に予測します。このツールは、RNAダイナミクスを分析するための分子動力学シミュレーションに代わる、高速でスケーラブルな選択肢を提供します。

キーワード:
3次元畳み込みニューラルネットワークRNAダイナミクス予測RNA局所柔軟性分子動力学シミュレーション

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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科学分野:

  • 計算生物学;構造生物学;バイオインフォマティクス

背景:

  • RNAの構造ダイナミクスを理解することは、その生物学的機能を解読するために不可欠です。静的構造からRNAの局所的な柔軟性を予測することは、依然として重大な計算上の課題です。既存の手法では、RNAの動的特性を効率的に予測することが困難です。

研究 の 目的:

  • RNAの振動柔軟性を予測するための深層学習ベースの手法、DeepRMSFを開発すること。RNAの局所ダイナミクスを評価するための計算効率の高いツールを提供すること。トランスクリプトーム全体にわたるRNA柔軟性の大規模な分析を容易にすること。

主な方法:

  • 原子レベルのRNA記述を利用した深層学習モデルであるDeepRMSFを開発しました。分子動力学（MD）シミュレーションから得られた二乗平均平方根変動（RMSF）に基づいてモデルをトレーニングしました。厳密な交差検証と独立したテストセットを使用して、371の非冗長なRNA構造でDeepRMSFをベンチマークしました。

主要な成果:

  • DeepRMSFは、独立したテストセットで高い相関（PCC〜0.73-0.75）でRNAの振動柔軟性を正確に予測します。柔軟性予測において、従来のMDシミュレーションと比較して3000倍以上の高速化を達成しました。中規模RNA（約75ヌクレオチド）に対して強力な外挿精度を示し、約8.2秒で柔軟性を予測しました。

結論:

  • DeepRMSFは、トランスクリプトーム全体にわたるRNA柔軟性スクリーニングのためのスケーラブルで実用的なアプローチを提供します。この手法はMDシミュレーションを補完し、RNAダイナミクスの分析のためのより高速な代替手段を提供します。RNAの構造-ダイナミクス-機能の関係のより深い理解を促進し、計算RNA生物学を支援します。